Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation

Background Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome. Results In the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL). Conclusion The identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-021-03408-5.


Background
Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are involved in physiological and biochemical reactions in plant growth, including lipid transport between cell membrane systems, inhibiting the growth of pathogens and signalling. nsLTPs are lowmolecular-weight cysteine-rich proteins and are widely distributed in the plant kingdom [1]. Their sequences are characterized by an 8-cysteine motif (ECM): C-Xn-C-Xn-CC-Xn-CXC-Xn-C-Xn-C [2]. The N-terminal of mature nsLTPs contains a signal peptide typically composed of 21-29 amino acid residues. In addition, some lipid transfer proteins (LTPs) also carried the motifs that add glycosylphosphatidylinositol (GPI)-anchors, which attach proteins to the outside of the plasma membrane [3]. The main feature of the spatial structure of plant nsLTPs is that H1-H4 are connected by four pairs of disulphide bonds that form a stable structure with a hydrophobic hole [4]. The hydrophobic parts of some lipids can interact with this hole. To date, many kinds of LTP genes have been isolated in many plants. Boutrot et al. had divided the LTPs into nine types according to sequence similarity [2]. Edstam et al. further classified the plant LTPs into four categories (1, 2, D, G) and several subclasses (C, E, X, etc.) according to the intron position, sequence identity, the distance between cysteine residues in the ECM, and the post-translational modifications [3].
The nsLTP family is ubiquitous and has been studied in many plants, such as in Arabidopsis thaliana, rice, Triticum kiharae and Brassica rapa [2,5,6]. nsLTPs are involved in a variety of physiological functions, such as the ability to enhance cell wall extension in tobacco and wheat [7][8][9][10]. In addition, Zhao et al. found that overexpression of the OsLTPL 159 IL 112 could enhance the cold tolerance of rice [11]. Transgenic plants overexpressing the StnsLTP1 gene acquire improved tolerance to multiple abiotic stresses through enhanced activation of antioxidative defence mechanisms [12]. Dhar et al. found an nsLTP gene was down-regulated in response to multiple bacterial pathogens, further research revealed that this nsLTP was required for defence against bacterial and fungal pathogens as well as for normal seedling growth under salinity stress, and it was named as disease-related nonspecific lipid transfer protein 1 (DRN1, 13]. Although its molecular mechanism is not clear, the responses of LTP genes in these studies suggested that nsLTPs are played an important role in plant stress resistance. Brassica napus is an important oil crop globally. Only a few studies have focused on single genes in nsLTP family, such as BraLTP1, a new nsLTP gene involved in wax production or deposition, it also has direct or indirect effects on cell division and flower development [13]. Another study found that a new nsLTP gene BraLTP2 might be involved in trichome development and the accumulation of secondary metabolites [14]. However, there has been no genome-wide analysis of nsLTP family in B. napus. After the reference genome of rapeseed cultivar 'Darmorbzh' was published in 2014, a higher-quality genome of the cultivar 'ZS11' was released in 2017 [15,16]. However, owing to the existence of structural variations, especially the presence/absence variations (PAV), the genome of a single cultivar cannot completely cover the entire gene catalogue. Pangenomes have been constructed for many species to obtain more genetic data resources, such as soybean, maize, rice, tomato [17][18][19][20][21]. In 2019, Song et al. constructed a high-quality pangenome of B. napus by using eight B. napus varieties [22,23]. In the present study, the nsLTP gene identification, characterization, and expression analysis were conducted by whole-pangenome, and a total of 246 nsLTP family genes were identified, and which could be classified into five types: 1, 2, C, D, G. We classified the nsLTPs belonging to the reference genome and non-reference regions, and present a more comprehensive understanding of nsLTP distribution in different varieties. The phylogeny, Ka/Ks, GO enrichment and expression of the nsLTP family were also analyzed. These results lay a foundation for further studies on the function of the LTP family in B. napus.

Identification of nsLTP genes in the B. napus pangenome
The pangenome sequence was downloaded from the B. napus pangenome information resource (http:// cbi. hzau. edu. cn/ bnapus/) [22]. The coding sequence (CDS) and protein sequences of the pangenome were obtained by gffread v0.12.7 with the pangenome sequences and annotations [24]. NsLTP sequences of A. thaliana were downloaded from TAIR (http:// www. arabi dopsis. org). The homologous nsLTPs genes between A. thaliana and B. napus were identified by comparing the CDS sequences to the A. thaliana nsLTPs sequences with blastx v 2.2.26 using a threshold of 1E-5. The Tryp_ alpha_amyl.hmm and LTP_2.hmm files in pfam [25] were downloaded, and hmmscan v3.3.1 was used to identify candidate LTP family genes with a threshold of 1E-5. After finding the candidate nsLTPs in two ways, the protein sequences were submitted to the conserved domain database (CDD) [26] and InterProScan (https:// www. ebi. ac. uk/ inter pro/ search/ seque nce/) to check for the presence of LTP domains.
An in-house perl script was then used to check for the presence of the ECM structure in the candidate LTP, and sequences with no ECM structure were removed. Then, we used SignalP v4.1 to predict the location of the signal peptides [27]. Sequences without signal peptides were also removed.

NsLTP sequence analysis
Two prediction tools, PredGPI (http:// gpcr2. bioco mp. unibo. it/ gpipe/ pred. htm) and GPI-SOM (http:// gpi. unibe. ch/), were used to determine the presence of C-terminal GPI-anchor sites. Sequences with GPIanchor sites were classified as category G, and the others were classified according to Edstam et al. [3]. A. thaliana nsLTP sequences were downloaded from TAIR, and B. napus LTP sequences were used to construct a phylogenetic tree. The multiple sequence alignment tool MEGA7 was used to generate a phylogenetic tree by the neighbour-joining method. MEME v2.0.0 [28] was used to analyse the conserved motifs in the B. napus nsLTP genes, with the highest number of motifs set to 10. Gene structures were visualized using GSDS 2.0 [29].

Gene duplication analysis, synonymous and non-synonymous substitution rates estimation
The duplication of genes can be divided into two types: tandem duplication and segmental duplication. The criterion for tandem duplication of LTP gene is that the physical distance of two genes on the chromosome should fall within 50 kb [30].
Segmental duplication refers to the case where the two genes are physically far away on the chromosome, but are still homologous. The criteria are as follows: (1) the region of overlap between homologous genes accounts for more than 80% of the total length of longer genes and (2) the sequence similarity is more than 80%. Synonymous and non-synonymous substitution rates of duplicated genes were calculated by TBtools v1.068 [31].

Cis-element analysis of the promoter regions of the nsLTP genes
In this study, in-house perl script was used to extract the upstream 2 kb sequence of BnLTP genes. The binding site prediction tool (http:// plant regmap. gao-lab. org/ bindi ng_ site_ predi ction. php in plantregmap) was used to predict TF binding sites in the 2 kb upstream sequence of BnLTPs.

Gene ontology (GO) annotation and enrichment analysis
All BnLTP sequences were compared with sequences in the uniprot database using blastp with a threshold of 1E-5. Using the Retrieve/ID mapping tool (https:// www. unipr ot. org/ uploa dlists/), uniprot IDs were converted to GO IDs to perform GO annotation for BnLTPs. AgriGO (http:// bioin fo. cau. edu. cn/ agriGO/ analy sis. php) was used for GO enrichment analysis. All genes of the Brassica napus pan-genome were used as the background gene set.
The RNA-seq clean data of each sample were aligned to the Brassica napus pan-genome using HiSAT2 v2.1.0. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values of genes in all samples were calculated as the expression level. The DESeq2 v1.32.0 [32] was used for differential expression analysis, and unigenes with |log2 ratio| ≥ 1 and q < 0.05 as a cut-off for significant differential expression were selected. The transformed log2 (FPKM + 1) values were used to generate the heatmap using R (version 4.0.3) with the Com-plexHeatmap package (version2.6.2, https:// bioco nduct or. org/ packa ges/ relea se/ bioc/ html/ Compl exHea tmap. html).
In the pangenome-wide search for nsLTP genes, BnLTP genes were identified on all chromosomes in the reference genome of ZS11 (Table S1), in which, 197 were located in the reference genome of ZS11 and 49 were located in non-reference regions. It was revealed that the BnLTPs were unevenly distributed on different chromosomes, C02 and C03 were with 18 BnLTPs, and only two LTPs were located on A04. According to PAV data, the LTP family genes identified in non-reference genomes were distributed across 13 chromosomes and A09 was with the most numbers (Fig. 1). The non-reference regions contained 1 (1), 2 (7), D (13) and G (23) types of BnLTPs with the number of 1, 7, 13 and 23, respectively. According to the PAV information, the BnLTPs were not evenly distributed in all varieties (Table 2), and the variety GG had the most of 13 BnLTP genes, otherwise, only 1 was observed in QU, it indicated that BnLTP genes may be lost in QU and duplicated in GG during domestication. The above results also suggested that when analysing the nsLTP gene family should not only focus on the reference genome.

Phylogenetic analysis and BnLTP sequence features of the B. napus
The neighbour-joining method was used to construct a phylogenetic tree based on the nsLTP sequences of B. napus and A. thaliana. The branching of the tree is consistent in general with the classification into the main structural types and indicates that nsLTP genes in each clade were originated from a common ancestor (Fig. 2), further analysis revealed that the types1, D, and G have two, five and eight sub-branches, respectively. According to Fig. 2, the typeD and G BnLTPs are closely related, since many sub-branches of typeD and G are very close in the phylogenetic tree. ECM sequence logos were constructed for each BnLTP type to explore which amino acid residues were conserved between adjacent cysteine residues. Figure 3 shows that type1, 2, and C are more conservative than that of typeD. The CXC structure can affect cysteine pairing and influence protein folding. Among all the BnLTP sequences, there were 12 different amino acid residues in the CXC structure: A, E, F, G, I, K, L, M, Q, R, V, and Y. Hydrophobic residue L was the most common residue in type2, D, and G. In type1, the proportions of R, K, Q, and E residues were similar.

Duplication patterns and synteny analysis of the BnLTP genes
Gene duplication is considered to be a driving force in evolution and an important factor to increase genome complexity. B. napus is an allotetraploid formed by natural interspecific hybridization and chromosome doubling between B. oleracea (CoCo, 2n = 18) and B. rapa (ArAr, 2n = 20, 16]. Therefore, there are usually two or more duplicated gene sequences in the genome of B. napus. Segmental and tandem duplications are considered to be the main reason why the gene family is expanded. In the present study, 22 pairs of tandem duplications were identified (Table S2), including two pairs in GG, three in SL, and 17 in ZS11. Among them, the A10 chromosome of Shengli had the highest number of tandem duplication events. It was revealed that three pairs of tandemly duplicated BnLTP genes (BnLTPD.43, BnLTPD. 44,BnLTPD.45) were all in the same duplicated gene blocks. Segmental duplications were identified by blastp with the requirement that there was > 80% overlap with the longer sequence, > 80% sequence similarity, and the repeated pairs are counted only once. A total of 339 segmental duplications BnLTP pairs (Table S3) were identified, including of 4 genes in D, 2 in TA, 1 in QU, 9 in NO, 3 in WE, 13 in GG, 7 in ZY and 7 in SL. Among them, the C03 chromosome of ZS11 had the highest number of segmental duplication events. We also analyzed the synteny of the BnLTP genes between the reference genome and non-reference regions (Fig. 4). Many variety-specific BnLTP genes were with a syntenic relationship with the BnLTP genes on the reference genome, such as 13 BnLTP in Gangan have syntenic relationship with the BnLTP genes on chromosomes A06, A07, A08 and A09 of the reference genome, and 11 Gangan-specific BnLTPs have a syntenic relationship with the BnLTP on the reference chromosomes of C04, C05, C07, C08 and C09 of B. napus C genome. In the varieties Quinta and Tapidor, only one specific gene maintained a syntenic relationship with BnLTP on the reference genome. This indicated that BnLTPs have different duplication patterns in different varieties.

Cis-regulatory factors and GO analysis of the LTP gene
Analysis of the 2 kb upstream regions (from the translation start site) of BnLTP genes could reveal the presence of various regulatory elements that are associated with the development and abiotic/biotic stress signalling. It was revealed that the ethylene-responsive factor (ERF) binding sites account for the largest proportion of sites in the upstream regions of the genes in the reference genome and non-reference region (Fig. 5), these sites are involved in hormonal signal transduction, response to biotic and abiotic stresses, regulation of metabolism, and developmental processes in various plant species. Weidong Wang et al. found that the upstream of LEA gene family in tea species is regulated by ERF, MYB and bZIP and bHLH transcription factor [42], which shows that the genes regulated by AP2/ERFs is a common phenomenon. Some other regulatory elements involved in the regulation of growth and development processes, such as the Dof (DNA binding with one finger) binding site, were also enriched in BnLTPs. The pathogen-and viral infection-responsive cis-regulatory elements included of the TF binding sites NAM, ATAF, and CUC (NAC) were also identified. Other regulatory elements, such as binding sites for C2H2 zinc finger transcription factor (involved in the occurrence of plant leaves and the regulation of floral organs) and lateral organ boundaries domain (LBD, involved in the development and formation of plant lateral organs), also existed.
To further understand the function of LTP in organisms, GO annotation and enrichment analysis of LTP genes were performed. Figure 6A shows that binding (GO:0005488) was the most abundant GO term that LTPs were identified as being involved in, which is consistent with the function of BnLTP. In the GO function enrichment analysis, significant enrichment was observed for a large number of GO terms related to binding and transport, such as lipid binding, fatty acid binding, monocarboxylic acid binding, lipid transport, and organic substance transport. Meanwhile, systemic acquired resistance and salicylic acid-mediated signalling pathways were also significantly enriched, which reveals that the nsLTP gene family was involved in biotic and abiotic stress responses. (Fig. 6B, C, D).   [43]. Compared to the mock-inoculated samples, only two BnLTPs were differentially expressed in R-line in 24 h after infection, while in S-line, 16 BnLTP genes were differentially expressed (Fig. 7A) in 24 h after infection. After 48 and 96 h of infection, the R and S lines showed similar numbers of differential expression genes. However, according to Fig. 7A and B, the response of BnLTPs to inoculated S. sclerotiorum was different at different periods in the two lines. In the R-line, there were no common differentially expressed BnLTP genes between the three periods, and 20 BnLTP genes were only found in 96 h after infection. In the S-line, only eight BnLTP genes were found in all three periods, and 16 BnLTP genes were only in 96 h after infection. The two lines were compared at different infection stages, and there were 44, 17, and 18 differentially expressed BnLTP genes 24, 48, and 96 h after infection (Fig. 7C), respectively, indicating that the response of BnLTP genes in the two varieties was the most different in the early stage of infection.
Log 2 (FPKM+ 1) values of the genes were used to plot the heatmap (Fig. 7D), it shows that some typeG BnLTP genes exhibited low expressions, but exhibited most differential expression. There were fewer type1 BnLTP genes than type2 BnLTP genes in the pangenome, but more differentially expressed type1 BnLTP genes than type2 BnLTP genes. Figure 7D shows the expression level of each differentially expressed BnLTP gene in the different samples. The expression of BnLTPG.7 and BnLTPG.72 genes was lower in the R-line than in the S-line.

Linking BnLTP genes to known QTL for blackleg resistance
To further assess possible biological functions of BnLTPs, we compared the position of BnLTPs with known QTL for blackleg resistance [44]. Positions were predicted from known genomic regions of seven loci in the ZS11 assembly. The QTL name and references are shown in Table 3. These QTLs covered between 5.3 Mb and 30.5 Mb on three pseudomolecules (Rlm1, Rlm3, Rlm4, Rlm7 and Rlm9 were located on A07, as well as LepR1 and LepR2 was located on A02 and A10 respectively). Furthermore, the mapping of Rlm4 covered the greatest number of BnLTPs which 1689 consist of 4 core and 4 variable genes. Rlm7 and Rlm9 loci contained only one variable BnLTP. The Rlm1 was the narrowest QTL but contained 5 BnLTPs which number was in the medium of all loci.
Song et al. combined rape resequencing data produced by several studies, then a large number of variations were identified [23]. Based on the mutation information, two waterfall plots of the blackleg-linked QTL (LepR1 locus, Rlm3 locus and Rlm4 locus) were produced to show the mutational load of BnLTPs located within the QTL candidate regions. We filtered BnLTPs without SNP and individuals without mutation in BnLTPs and finally showed the mutation load of 773 individuals in Rlm3 and Rlm4 loci as well as 1283 individuals in LepR1. Moreover, the loci of Rlm3 and Rlm4 covered the same BnLTPs thus their waterfall plots are identical (Fig. 8). As shown in the waterfall plot of Rlm3 and Rlm4 loci, the maximum and minimum mutation percentages were related to BnLTPG3.1 and BnLTP2. 22, respectively (Fig. 8A). BnLTP2.11 exhibited the highest mutation in all BnLTPs located on LepR1 locus, and

Discussion
In this study, 246 BnLTP genes were identified, including of 29 type1, 50 type2, four typeC, 48 typeD, and 114 typeG in the entire pangenome of rapeseed. In addition to the 197 BnLTPs found in the reference genome, another 49 BnLTPs in the non-reference region of the non-reference sequences also existed. In the study of Hurgobin et al. [45], 53 synthetic and nonsynthetic accessions were used to generate the first B. napus pangenome. 13,631 new genes were predicted in the pangenome. We compared the 13,631 genes with the pan-genome published by Song et al. [22] using the software BLASTN with the parameters'-e 1emur10' and'-F F 'and a sequence identity of > 98%. Finally a new nsLTP gene was identified uniquely in the 13,631 genes. It indicates that more members of gene family may be found in the genomic data resources of more varieties, and more nsLTP genes can be discovered on the basis of this study in the future. In different cultivated species, the distribution of BnLTPs in the non-reference region was not balanced, which indicated that the different varieties underwent different forms and levels of selection during domestication. In the reference genome, the identified BnLTPs were unevenly distributed across the genome. The uneven distribution of BnLTPs might be due to recent BnLTP gene tandem duplications, segmental duplications and dosage compensation, which is critical for development and phenotypic characteristics [44]. The results show that the order and proximity of genes of the gene family are important to the functional nature of these genes [44]. are not present in the reference genome [45]. The present study and the above mentioned two pangenome studies showed that it is necessary to identify candidate genes in the pangenome for breeding work, as it can avoid the disadvantage of having incomplete information on a single reference genome. Among the identified BnLTPs, 22 and 339 pairs were tandem duplicates and segmental duplicates, respectively, it indicated that the gene duplications played an important role in the expansion and evolution of nsLTP residence in rapeseed. This phenomenon is not only found in rape, but also in other species, e.g., A. thaliana, turnip, rice, and maize [2,6,47]. In this study, the phylogenetic relationships of nsLTPs between B. napus and the A. thaliana showed a high degree of consistency in the same type between the two species.
Previous studies have shown that the nsLTPs are involved in a variety of biotic and abiotic stress responses [5,48] .Odintsova et al. speculated that nsLTPs are involved in the activation of pathogen defences [5]. Their mechanisms of action might be due either directly to the antimicrobial or lipid-transferring activity or indirectly as signalling molecules [5]. Another study found that overexpression of AtLTP4.4 could protect against the oxidative stress that induced by trichothecene by increasing the glutathione-based antioxidant defence effect [49]. These results suggested that the nsLTP family might play an important biological role in plant responses to pathogen infection. In order to study the role of BnLTP in the response to S. sclerotiorum, we analyzed the sequencing data (accession no. SRP053361) of two rape varieties (a resistant line and a susceptible line) under S. sclerotiorum infection for 24, 48, and 96 h [43], it was revealed that the sixty-one BnLTPs were identified to be differentially expressed in different samples, which also indicated that different BnLTP types have different expression patterns (Fig. 7D).
The experiment in vitro showed that nsLTPs are involved in many plant disease resistance. In some in vitro studies, heterologous expression and purification of nsLTPs showed resistance to a variety of plant pathogens [50,51]. nsLTP is a plant disease-related protein (PRs) and the expression level increased with the inducing of pathogenic bacteria as well as inhibit the reproduction of pathogenic bacteria and induce the resistance-related response in plants [51]. By some biochemical methods and overexpression or knockout experiments, it was demonstrated that some nsLTPs are playing important role in resisting the invasion of pathogens [52][53][54]. For example, Patar et al. overexpressed the onion (Allium cepa) Ace-AMP1 in rice, which improved the resistance of rice blast, sheath blight and parabola without changing other agronomic traits [50]. Overexpressed wheat Ltp 3F1 in tobacco improved plant resistance to fungal diseases [51]. Inhibiting the expression of CALTPI and CALTPII in pepper, transgenic plants showed susceptibility to bacterial diseases. After overexpressing CALTPI and CALTPII in tobacco, disease resistance improved and the degree of disease resistance increased with the expression level of CALTPI and CALTPII [55]. nsLTPs were reported to have a certain role in plant disease resistance signal pathways. Maldonado et al. found that Arabidopsis nsLTP (DIR1) was involved in the process of an important mobile signal production or transmission in leaf which was infected with Phytophthora syringae [56]. Furthermore, they proposed that DIR1 interacts with a lipid-derived molecule to promote long-distance signal transmission. Grafting wild type tobacco and CALTPI and CALTPII overexpressed tobacco showed that the CALTP participates in long-distance system signaling transmission and plays an important role in the interaction of plant pathogens by activating SAR-mediated signaling pathway [55]. The above studies showed that nsLTPs play an important role in the resistance of plants and the invasion of a variety of pathogens. To further assess possible disease resistance-related functions of BnLTPs, we compared the position of BnLTPs with known QTL for blackleg resistance [44]. The blackleg resistance QTLs contained 14 core and variable BnLTP genes. Two genes (BnLTPG. 10 and BnLTPG.12) showed the lowest mutation in the LepR1 locus but had a large number of missense variants, it may be indicative that these genes were under positive selection pressure (Fig. 8B). There was a more synonymous variants that occurred on LepR1 locus compared with Rlm3 and Rlm4 loci, revealing that LepR1 locus is more stable than Rlm3 and Rlm4 loci. Identification of BnLTPs within QTL may provide a basis for Brassica napus breeding in the future. According to previous studies, CNVs (copy number variations) are major genetic variations influencing gene expression and phenotype. There are more CNVs than chromosome structural variations, and the total number of nucleotides covered by CNVs is much larger than SNP number in the whole genome [57,58]. Therefore, in the future research, we will analyze the impact of CNVs on